Ewan Birney

NAME

Bio::AlignIO - Handler for AlignIO Formats

SYNOPSIS

    use Bio::AlignIO;

    $inputfilename = "testaln.fasta";
    $in  = Bio::AlignIO->new(-file => $inputfilename , '-format' => 'fasta');
    $out = Bio::AlignIO->new(-file => ">out.aln.pfam" , '-format' => 'pfam');
    # note: we quote -format to keep older perl's from complaining.

    while ( my $aln = $in->next_aln() ) {
        $out->write_aln($aln);
    }

or

    use Bio::AlignIO;

    $inputfilename = "testaln.fasta";
    $in  = Bio::AlignIO->newFh(-file => $inputfilename , '-format' => 'fasta');
    $out = Bio::AlignIO->newFh('-format' => 'pfam');

    # World's shortest Fasta<->pfam format converter:
    print $out $_ while <$in>;

DESCRIPTION

Bio::AlignIO is a handler module for the formats in the AlignIO set (eg, Bio::AlignIO::fasta). It is the officially sanctioned way of getting at the alignment objects, which most people should use. The resulting alignment is a Bio::Align::AlignI compliant object. See Bio::Align::AlignI for more information.

The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular AlignIO object instance is configured for either input or output. A specific example of a stream object is the Bio::AlignIO::fasta object.

Each stream object has functions

   $stream->next_aln();

and

   $stream->write_aln($aln);

also

   $stream->type() # returns 'INPUT' or 'OUTPUT'

As an added bonus, you can recover a filehandle that is tied to the AlignIO object, allowing you to use the standard <> and print operations to read and write sequence objects:

    use Bio::AlignIO;

    $stream = Bio::AlignIO->newFh(-format => 'Fasta'); # read from standard input

    while ( $aln = <$stream> ) {
        # do something with $aln
    }

and

    print $stream $aln; # when stream is in output mode

This makes the simplest ever reformatter

    #!/usr/local/bin/perl

    $format1 = shift;
    $format2 = shift || die "Usage: reformat format1 format2 < input > output";

    use Bio::AlignIO;

    $in  = Bio::AlignIO->newFh(-format => $format1 );
    $out = Bio::AlignIO->newFh(-format => $format2 );
    #note: you might want to quote -format to keep older perl's from complaining.

    print $out $_ while <$in>;

AlignIO.pm is patterned on the module SeqIO.pm and shares most the SeqIO.pm features. One significant difference currently is that AlignIO.pm usually handles IO for only a single alignment at a time (SeqIO.pm handles IO for multiple sequences in a single stream.) The principal reason for this is that whereas simultaneously handling multiple sequences is a common requirement, simultaneous handling of multiple alignments is not. The only current exception is format "bl2seq" which parses results of the Blast bl2seq program and which may produce several alignment pairs. This set of alignment pairs can be read using multiple calls to next_aln.

Capability for IO for more than one multiple alignment - other than for bl2seq format -(which may be of use for certain applications such as IO for Pfam libraries) may be included in the future. For this reason we keep the name "next_aln()" for the alignment input routine, even though in most cases only one alignment is read (or written) at a time and the name "read_aln()" might be more appropriate.

CONSTRUCTORS

Bio::AlignIO->new()

   $seqIO = Bio::AlignIO->new(-file => 'filename',   -format=>$format);
   $seqIO = Bio::AlignIO->new(-fh   => \*FILEHANDLE, -format=>$format);
   $seqIO = Bio::AlignIO->new(-format => $format);

The new() class method constructs a new Bio::AlignIO object. The returned object can be used to retrieve or print BioAlign objects. new() accepts the following parameters:

-file

A file path to be opened for reading or writing. The usual Perl conventions apply:

   'file'       # open file for reading
   '>file'      # open file for writing
   '>>file'     # open file for appending
   '+<file'     # open file read/write
   'command |'  # open a pipe from the command
   '| command'  # open a pipe to the command
-fh

You may provide new() with a previously-opened filehandle. For example, to read from STDIN:

   $seqIO = Bio::AlignIO->new(-fh => \*STDIN);

Note that you must pass filehandles as references to globs.

If neither a filehandle nor a filename is specified, then the module will read from the @ARGV array or STDIN, using the familiar <> semantics.

-format

Specify the format of the file. Supported formats include:

   fasta       FASTA format
   pfam        pfam format
   selex       selex (hmmer) format
   stockholm   stockholm format
   prodom      prodom (protein domain) format
   clustalw    clustalw (.aln) format
   msf         msf (GCG) format
   mase        mase (seaview) format
   bl2seq      Bl2seq Blast output
   nexus       Swofford et al NEXUS format
   pfam        Pfam sequence alignment format
   phylip      Felsenstein's PHYLIP format

Currently only those formats which were implemented in Bio::SimpleAlign have been incorporated in AlignIO.pm. Specifically, mase, stockholm and prodom have only been implemented for input.

If no format is specified and a filename is given, then the module will attempt to deduce it from the filename. If this is unsuccessful, Fasta format is assumed.

The format name is case insensitive. 'FASTA', 'Fasta' and 'fasta' are all supported.

Bio::AlignIO->newFh()

   $fh = Bio::AlignIO->newFh(-fh   => \*FILEHANDLE, -format=>$format);
   $fh = Bio::AlignIO->newFh(-format => $format);
   # etc.

This constructor behaves like new(), but returns a tied filehandle rather than a Bio::AlignIO object. You can read sequences from this object using the familiar <> operator, and write to it using print(). The usual array and $_ semantics work. For example, you can read all sequence objects into an array like this:

  @sequences = <$fh>;

Other operations, such as read(), sysread(), write(), close(), and printf() are not supported.

OBJECT METHODS

See below for more detailed summaries. The main methods are:

$alignment = $AlignIO->next_aln()

Fetch an alignment from a formatted file.

$AlignIO->write_aln($aln)

Write the specified alignment to a file..

TIEHANDLE(), READLINE(), PRINT()

These provide the tie interface. See perltie for more details.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org               - General discussion
  http://bio.perl.org/MailList.html   - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Peter Schattner

Email: schattner@alum.mit.edu

CONTRIBUTORS

Jason Stajich, jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $stream = Bio::AlignIO->new(-file => $filename, -format => 'Format')
 Function: Returns a new seqstream
 Returns : A Bio::AlignIO::Handler initialised with the appropriate format
 Args    : -file => $filename 
           -format => format
           -fh => filehandle to attach to

newFh

 Title   : newFh
 Usage   : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format')
 Function: does a new() followed by an fh()
 Example : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format')
           $sequence = <$fh>;   # read a sequence object
           print $fh $sequence; # write a sequence object
 Returns : filehandle tied to the Bio::AlignIO::Fh class
 Args    :

fh

 Title   : fh
 Usage   : $obj->fh
 Function:
 Example : $fh = $obj->fh;      # make a tied filehandle
           $sequence = <$fh>;   # read a sequence object
           print $fh $sequence; # write a sequence object
 Returns : filehandle tied to the Bio::AlignIO::Fh class
 Args    :

_load_format_module

 Title   : _load_format_module
 Usage   : *INTERNAL AlignIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns : 
 Args    :

next_aln

 Title   : next_aln
 Usage   : $aln = stream->next_aln
 Function: reads the next $aln object from the stream
 Returns : a Bio::Align::AlignI compliant object
 Args    : 

write_aln

 Title   : write_aln
 Usage   : $stream->write_aln($aln)
 Function: writes the $aln object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq object

_guess_format

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function: 
 Example : 
 Returns : guessed format of filename (lower case)
 Args    :